[日本語] English
万見
- PDB-9b7h: Crystal structure of the H3 hemagglutinin COBRA TJ2 -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 9b7h
タイトルCrystal structure of the H3 hemagglutinin COBRA TJ2
要素
  • Hemagglutinin
  • Hemagglutinin HA1
キーワードVIRAL PROTEIN / hemagglutinin / antigen / receptor binding / membrane fusion
機能・相同性
機能・相同性情報


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
類似検索 - 分子機能
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
類似検索 - ドメイン・相同性
生物種Influenza A virus (A型インフルエンザウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.15 Å
データ登録者Dzimianski, J.V. / DuBois, R.M.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 米国
引用ジャーナル: J Virol / 年: 2025
タイトル: Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins.
著者: John V Dzimianski / Kaito A Nagashima / Joseph M Cruz / Giuseppe A Sautto / Sara M O'Rourke / Vitor H B Serrão / Ted M Ross / Jarrod J Mousa / Rebecca M DuBois /
要旨: Influenza virus infections are an ongoing seasonal disease burden and a persistent pandemic threat. Formulating successful vaccines remains a challenge due to accumulating mutations in circulating ...Influenza virus infections are an ongoing seasonal disease burden and a persistent pandemic threat. Formulating successful vaccines remains a challenge due to accumulating mutations in circulating strains, necessitating the development of innovative strategies to combat present and future viruses. One promising strategy for attaining greater vaccine effectiveness and longer-lasting protection is the use of computationally optimized broadly reactive antigens (COBRAs). The COBRA approach involves antigen design by generating iterative, layered consensus sequences based on current and historic viruses. Antigens designed by this process show a greater breadth of antibody-mediated protection compared to wild-type antigens, with effectiveness that often extends beyond the sequence design space of the COBRA. In particular, the use of COBRA hemagglutinin (HA) proteins has led to the discovery of broadly reactive antibodies that are suggestive of their therapeutic potential. Understanding the extent to which these antibodies are effective is key to assessing the resilience of vaccine-induced immunity to diverging influenza strains. To investigate this, we tested the binding of broadly reactive antibodies with a diverse panel of H3 HA proteins. Using cryo-electron microscopy, we defined the molecular characteristics of binding for these antibodies at the paratope-epitope interface. Through sequence and structural comparisons, we observed the correlative patterns between antibody affinity and antigen structure. These data shed light on the breadth and limitations of broadly reactive antibody responses in the context of an ever-changing landscape of influenza virus strains, yielding insights into strategies for universal vaccine design.IMPORTANCEFormulating effective influenza vaccines remains a challenge due to a constantly changing landscape of circulating viruses. This is particularly true for H3N2 viruses that undergo a high degree of antigenic drift. Several new vaccine designs can elicit broadly neutralizing antibodies that are effective against a range of influenza strains. More insight is needed, however, into how resilient these antibodies will be to future strains that evolve in the context of this selective pressure. Here, we measured the precise binding characteristics of three broadly neutralizing antibodies to 18 different hemagglutinin (HA) proteins representing almost 50 years of virus evolution. Using single-particle cryo-electron microscopy and X-ray crystallography, we determined the structural characteristics of the epitopes bound by these antibodies and identified specific amino acids that greatly impact the effectiveness of these antibodies. This provides important insights into the longevity of antibody efficacy that can help guide design choices in next-generation vaccines.
履歴
登録2024年3月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年5月7日Provider: repository / タイプ: Initial release
改定 1.12025年8月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22025年10月8日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: Hemagglutinin HA1
B: Hemagglutinin HA1
C: Hemagglutinin HA1
a: Hemagglutinin
b: Hemagglutinin
c: Hemagglutinin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)183,07832
ポリマ－170,1926
非ポリマー12,88626
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)77.252, 117.678, 198.617
Angle α, β, γ (deg.)90.000, 90.950, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and resid 9 through 325)
d_2ens_1(chain "B" and resid 9 through 325)
d_3ens_1(chain "C" and resid 9 through 325)
d_1ens_2(chain "F" and (resid 501 through 502 or resid 504...
d_2ens_2(chain "G" and (resid 496 through 497 or resid 499...
d_1ens_3(chain "a" and resid 330 through 500)
d_2ens_3chain "b"
d_3ens_3(chain "c" and resid 330 through 500)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERGLUGLUAA9 - 3253 - 319
d_21ens_1SERSERGLUGLUBB9 - 3253 - 319
d_31ens_1SERSERGLUGLUCC9 - 3253 - 319
d_11ens_2NAGNAGNAGNAGIL2
d_12ens_2NAGNAGNAGNAGBX401
d_13ens_2NAGNAGNAGNAGKN1
d_14ens_2NAGNAGNAGNAGKN2
d_15ens_2NAGNAGNAGNAGJM2
d_16ens_2NAGNAGNAGNAGLO1
d_17ens_2NAGNAGNAGNAGMP1
d_18ens_2NAGNAGNAGNAGMP2
d_19ens_2MANMANMANMANMP4
d_110ens_2MANMANMANMANJM4
d_111ens_2MANMANMANMANJM5
d_112ens_2NAGNAGNAGNAGBZ403
d_21ens_2NAGNAGNAGNAGNQ1
d_22ens_2NAGNAGNAGNAGNQ2
d_23ens_2NAGNAGNAGNAGOR1
d_24ens_2NAGNAGNAGNAGOR2
d_25ens_2NAGNAGNAGNAGCAA501
d_26ens_2NAGNAGNAGNAGPS2
d_27ens_2NAGNAGNAGNAGQT1
d_28ens_2NAGNAGNAGNAGCBA502
d_29ens_2MANMANMANMANNQ4
d_210ens_2MANMANMANMANOR4
d_211ens_2MANMANMANMANOR5
d_212ens_2NAGNAGNAGNAGRU2
d_11ens_3GLYGLYPHEPHEaD330 - 5001 - 171
d_21ens_3GLYGLYPHEPHEbE330 - 5001 - 171
d_31ens_3GLYGLYPHEPHEcF330 - 5001 - 171

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.19626453671, -0.435891366764, 0.878338743317), (-0.726846040514, 0.665920543526, 0.168061486068), (-0.658160364212, -0.605432528108, -0.447522500987)-32.7425329303, -30.9520274369, -76.5871398254
2given(-0.212941528197, -0.728564537032, -0.651037342208), (-0.438450018099, 0.666716680406, -0.60270262128), (0.873165211857, 0.15710691725, -0.461410803248)-79.7363512165, -39.9898125181, -1.28483606144
3given(0.232559930102, -0.354913795601, -0.905512052158), (-0.488984497839, -0.847477271756, 0.206582755162), (-0.840719953245, 0.394738485011, -0.3706365992)-85.8817155059, -33.8880582642, -68.3466992987
4given(-0.216369022318, -0.453974089556, 0.864344822506), (-0.720558985037, 0.671625370009, 0.17237781598), (-0.6587709733, -0.585514208514, -0.472434033877)-34.1006055675, -30.4803830497, -76.3538470858
5given(-0.198482399269, -0.711950832852, -0.67359538952), (-0.439880689394, 0.678870882904, -0.587910965575), (0.875847998387, 0.17961162531, -0.447917344802)-79.1890699598, -39.4282824589, -0.275550820623

-
要素

-
タンパク質 , 2種, 6分子 ABCabc

#1: タンパク質 Hemagglutinin HA1


分子量: 35885.355 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (A型インフルエンザウイルス)
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
#2: タンパク質 Hemagglutinin


分子量: 20845.256 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (A型インフルエンザウイルス)
遺伝子: HA
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: A0FCI1

-
糖 , 5種, 25分子

#3: 多糖
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 7 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
非ポリマー , 1種, 1分子

#8: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3

-
詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.65 Å3/Da / 溶媒含有率: 53.62 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M Tris pH 8.5, 21% PEG 3350

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-D / 波長: 1.03 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年7月27日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.03 Å / 相対比: 1
反射解像度: 3.15→45.66 Å / Num. obs: 30774 / % possible obs: 99.7 % / 冗長度: 3.8 % / Biso Wilson estimate: 96.19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.092 / Rrim(I) all: 0.181 / Χ2: 0.94 / Net I/σ(I): 6 / Num. measured all: 115794
反射 シェル解像度: 3.15→3.32 Å / % possible obs: 99.8 % / 冗長度: 3.9 % / Rmerge(I) obs: 1.424 / Num. measured all: 17421 / Num. unique obs: 4475 / CC1/2: 0.578 / Rpim(I) all: 0.828 / Rrim(I) all: 1.651 / Χ2: 0.94 / Net I/σ(I) obs: 0.9

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
Aimlessデータスケーリング
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.15→45.66 Å / SU ML: 0.5062 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.258
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2693 1470 4.78 %
Rwork0.2219 29264 -
obs0.2241 30734 99.59 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 107.22 Å2
精密化ステップサイクル: LAST / 解像度: 3.15→45.66 Å
タンパク質核酸リガンド溶媒全体
原子数11587 0 852 0 12439
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003212675
X-RAY DIFFRACTIONf_angle_d0.515717159
X-RAY DIFFRACTIONf_chiral_restr0.04992064
X-RAY DIFFRACTIONf_plane_restr0.00432150
X-RAY DIFFRACTIONf_dihedral_angle_d4.51422092
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.684016034315
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.596616667618
ens_2d_2GEX-RAY DIFFRACTIONTorsion NCS42.3606688296
ens_3d_2DaX-RAY DIFFRACTIONTorsion NCS0.916989969587
ens_3d_3DaX-RAY DIFFRACTIONTorsion NCS0.657237542907
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.250.40111450.37132647X-RAY DIFFRACTION99.39
3.25-3.370.38471370.32442665X-RAY DIFFRACTION99.72
3.37-3.50.3451470.30022611X-RAY DIFFRACTION99.86
3.5-3.660.33921520.27312630X-RAY DIFFRACTION99.53
3.66-3.850.27981220.26612653X-RAY DIFFRACTION99.75
3.85-4.10.29141150.23282669X-RAY DIFFRACTION99.86
4.1-4.410.27671200.20692675X-RAY DIFFRACTION99.5
4.41-4.860.2531420.20432670X-RAY DIFFRACTION99.72
4.86-5.560.24691410.20272657X-RAY DIFFRACTION99.71
5.56-70.25851280.21162659X-RAY DIFFRACTION99.25
7-45.660.19771210.17382728X-RAY DIFFRACTION99.23
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.592610228412-1.592095847970.7101108821363.53356222246-1.551961599691.05788751208-0.159025659233-0.1184334063830.184458610380.8260533391260.0223371177874-0.601662447584-0.3875263524870.06981920930570.1058698721280.706684927504-0.0948377748259-0.03012537744210.658411377536-0.02014493294090.874597444369-18.5908547545-18.8398825733-14.2204092509
21.45158143014-1.51081861377-0.3708597970095.50310322844-1.873711508082.588540085530.1564261417920.2304905639090.3372887107040.966293249286-0.272134283720.138692347889-1.274532918540.1455666528680.041999612450.96850626383-0.114750054970.01648896223250.924377731858-0.08769826107071.02677213236-30.72451732456.09358922435-24.1535912032
30.78603971353-1.353382338440.1725817729872.48435495911-0.9968269007232.050025012030.07554279838730.05811714844010.6335238985380.261735977283-0.124959561742-0.29606859301-0.9356754810140.190553779360.08417349332181.35900959819-0.083763069330.07890593989781.01919503376-0.141404716951.15402066761-33.066868936324.7785807916-29.9496110669
41.37677049171-0.8796215893340.3731834843691.85143576859-1.852948937922.517019685880.525435679186-0.0502460005611-0.046305712549-0.472105732094-0.0207675487499-0.66116313813-0.514140659251-0.173138773105-0.09971167539020.914997609826-0.02428535009340.0381188863090.802589236911-0.171172908221.15342490056-33.39930818911.6289939129-39.8559069186
50.336827025324-0.7435426637760.4074723830731.84118320757-0.7540185206410.369446037110.361050000234-0.579949418438-0.4902617647360.878212725157-0.371102028478-0.112662601242-1.03340792787-0.100224168153-0.2100311118831.459334282230.2791671525090.03451674933581.30236639187-0.07608873674861.2975276719-47.824105509325.7714667781-27.9824728341
61.93493924276-1.556767926161.114420195982.24799127641-1.424297236324.221373292510.184741100298-0.277273891634-0.0009179634242240.4391614110350.729074022515-0.2999891061020.00454214529621-0.431974957289-0.3766876902330.9602246133990.04989929507320.02191148544761.04255976504-0.097862931771.05659875944-44.319803558314.0868668838-28.7011875429
71.74967240804-1.737441244160.7802600213672.38240128007-1.817163771042.132886412270.07930444982830.161528521248-0.0776437430477-0.482058905195-0.00737171531163-0.100583598482-0.106436190211-0.194530936139-0.2178610877320.9686613129570.02930851832730.1112759365730.6576837947040.001267890792561.09665572942-37.86133635269.98104328694-37.6031210773
80.834415759086-0.8318094731690.8364883822062.07690770829-1.651937755062.916481964290.0504932319172-0.3390630907450.08177412919140.0314371872225-0.145168503628-0.337985710213-0.273917404924-0.176191314903-0.06044899149960.932382739262-0.01884925442690.106687435710.686556747906-0.1571760118251.05352315324-27.49573385464.37727658949-27.8345577274
91.74895218191-0.5082409729511.147562676071.78291666226-0.1691822209632.40823768123-0.1130266466841.0518305286-0.004399973935270.1157341029180.441240255346-0.660201427921-0.19640477666-0.208888804548-0.08953233278890.789753421995-0.0989561442658-0.008845191445020.794722222303-0.09762312401261.03503169506-20.4263806084-17.0545639118-16.6136577052
104.24734703553-4.137989968641.55719678992.90615047821-1.835655273051.66791510054-0.160027031642-0.496360377650.1210361172580.4343452619060.341681141715-0.1268058515510.306017057688-0.2467804191510.02301646752530.963305724428-0.0706049375484-0.04675833117020.862465088415-0.07439147084760.993918806951-19.3502605238-39.4508400663-6.56734710552
112.35294013029-3.053565049850.6123693341614.20538154367-0.9581311301690.6362918345010.1394164154710.040757846232-0.0906403378656-0.479696030284-0.0530390203666-0.05430484412890.135839756363-0.154639909247-0.09224537444350.844087778797-0.1510208791110.005726694402781.01233414738-0.07253103249180.982455494571-35.1750347074-28.0550864939-47.3566234986
125.05542035199-1.00162630230.5035909052054.11622599424-1.021286740562.99202217530.2247240005290.317811370408-0.906188074915-0.7108585470890.1209524695370.165470688121-0.606841036144-0.957657680143-0.1186232768140.8684950879770.041397492776-0.1338963750081.431058837310.01508730552090.848773781183-55.0017728079-13.5726413608-46.5763264218
132.91636768685-0.127215256857-0.3828247433013.23794221945-0.4370602786842.05488571140.2905586683390.510927205208-0.226337939885-1.16365123294-0.4635944323510.407251874483-0.300080411672-1.424006688410.0221749677381.118339000820.203827522576-0.1333462728151.283431193530.03992113870721.01008670414-62.11153648812.12314802628-58.7341503289
143.86027602225-0.841700493103-1.062604746472.595490838890.139127899342.526883209610.266693435125-0.5152944703640.01029697623340.119096080266-0.6018682789480.706988493982-0.194825535141-0.840794893685-0.0003813685388440.724789476527-0.0446042933636-0.171979741071.612399127010.1056179860430.940174703102-67.29493983950.669647179214-49.3861489082
154.57904954463-0.205265449142-1.099676158494.62186308528-0.8051075343122.762206959720.296624814523-0.2405843859590.750705613856-0.361816028317-0.1346722184280.375093428665-0.345978432466-0.802780127229-0.0992191757380.8398640499850.138489670329-0.03282085942741.21101234465-0.02100599490340.957035292926-57.30026361097.57764815209-45.1181034404
163.08291839721-1.03301636928-0.7434613929283.488379954120.9251100825351.47377474581-0.115782598404-0.416633124908-0.2177687691820.04966075763140.1490174762510.5396798754450.154064345035-0.919272791316-0.059588288230.709302248003-0.0389799427726-0.03638137734161.263169000020.1333329521190.78480081636-57.4878453857-8.70784769479-45.31660076
172.47875992509-2.419944304351.090557009272.40901225308-2.150694036344.298701405340.165894928662-0.201807572173-0.71009673532-0.195047176698-0.335647550522-0.1024843868340.99372161266-0.542608131408-0.2518131030881.05815137505-0.29450202521-0.01830630890480.81654464463-0.01466972019761.02511809368-36.3164142074-30.0885351537-46.0872206577
182.62224676641-5.747522268320.8722272623066.15743154914-0.7077190758821.315934245890.0592162144219-0.2135998692560.339522509576-0.585343509458-0.0287096702154-0.5812026401760.1623998688360.01449990381750.007987092611610.764853561827-0.1555463688830.1761317404310.7754733732430.007556278083241.01164788099-20.4796720757-41.7267852033-37.4935356023
191.35491008052-1.560888569830.200735047922.59077255757-0.3141467381790.654111420349-0.207563948218-0.036079916667-0.4150785083650.3033756237380.1759837423370.9404403075720.0504211172752-0.55910398002-0.01165133105940.787999758836-0.1078763523260.1154939109061.2555167658-0.03820413201150.994807885953-58.2723626502-22.0255052471-13.8185875107
201.832553965290.119198081371-0.7078734874841.80773096630.1375643006231.62566579741-0.106475005505-0.6156660866120.3004812718-0.05096258508410.06558574972240.319789001118-0.272098188426-0.765883670169-0.01783478522630.9929878523610.1604674617140.1495294875291.29743901623-0.04283024215341.04629693174-61.7821672878.60456967438-18.1850584194
211.07888036862-1.34410365885-0.4050330863143.0295923770.5751371470771.01946445617-0.126437658087-0.247510649618-0.2533449022740.2059360395780.2169371592150.423174069310.161354425866-0.566309098772-0.1287158947120.760542235345-0.1130981742270.04248556589061.23660073310.04623161568040.937126780191-52.3524920876-28.3618451426-14.7237204822
223.58164178079-3.070804512031.850101666512.50490457942-1.764604223892.18990996915-0.397961731803-0.08491579478930.02627261200290.0979274802410.205843414392-0.3762739361660.0274818391808-0.2957300713930.1377520616830.875549095301-0.0835480424544-0.02578973045290.7420692092050.01560956234661.0070375989-6.31481403809-52.2167963788-10.1480786269
230.394925070845-1.092674456220.8545334769321.46849178969-1.117508103160.752150587345-0.186538152185-0.328515499060.127700524176-0.6123940144140.0334863812475-0.7025880458810.248207720890.2177918536980.01720931765260.791649315423-0.1659566985620.03398523567981.05910715813-0.03807443073221.27905404886-19.2282140475-24.072111623-24.6722613867
241.38295369575-2.318851083670.7369571784985.04073916311-1.61961591030.896572212824-0.0991451106928-0.031247204072-0.01911852702870.2226915000290.1722098698790.05053479482410.0183606749177-0.200441707791-0.2353748271310.673063468787-0.1459177418380.03877743887760.716446682275-0.007522261796620.785935618024-27.129091657-33.0782334921-18.0472414942
252.54904956796-1.522802296381.430920114884.25162676097-1.133479799941.70489111364-0.244213336663-0.0309260948148-0.307417198748-0.6219613935470.118312855885-0.05230467728380.5483021745960.5894996566920.03954975717981.06898229848-0.02893321606060.06827920744290.8672941503410.03592276454531.050450835460.207889364091-71.7450514999-12.8123812643
262.50993589238-2.31423433841-0.2838604547626.153152252160.9248507793151.80044947220.12121215820.033022542204-0.4969132879-0.642557280142-0.2104521037570.5738553158251.08829413812-0.1873277597530.1116260763721.05197916336-0.188233821610.1112896707160.674543059963-0.08523714991430.798964372248-18.6451883949-61.7942479546-36.5278499704
276.04605862815-2.375572775041.499132882810.8602543858780.1753302033923.57443935329-0.5426010031021.19769622677-0.661025061798-0.186376661491.22010860323-0.64546591040.231327064388-0.276641430096-0.06369570351380.83089603413-0.1578352138320.1178492568450.971248597534-0.1463095717760.792375635699-39.8693899131-21.3894732848-38.8556956882
281.19092591089-3.043090849520.3167157132926.65638684425-0.7709722735130.4383306793050.1416458780740.156254029152-0.000183542898019-0.494133430266-0.2523696633960.317104434880.466622263093-0.04705245596840.1295308364560.887490502089-0.1593087241010.08262322523440.675825928084-0.08117200750970.881371917237-20.2269458542-59.8616843675-28.7568439102
292.0566279901-1.99395083961-1.050033267892.298060265930.3783350166451.79020560752-0.661164405673-0.167159459266-0.475211984416-0.9601660217420.5457921206280.6301384186340.792408702927-0.331200115490.03983360192891.20338702629-0.286265596976-0.006059025878420.8391546451830.0537907514631.19199038918-34.2256579698-66.5093542925-15.8485827194
305.2153202318-3.38501680088-0.6204286035855.250774736160.0674725651543.71576628728-0.674508591995-0.358402632106-0.02295301128170.9933087996960.709109741083-0.3616520253970.543811063107-0.0936247058478-0.02876146808340.784951299589-0.282464756179-0.01928190073270.9486539556550.02620773692420.810102749707-33.5579105682-65.6000032894-6.74533389401
31-0.115096033782-0.4041369038250.2271634100811.3570430977-0.7166698099480.43861054608-0.200263226978-0.45752444431-0.06086356130830.9721134996460.524671368604-0.911890103525-0.218042483281-0.256412422504-0.0850110484681.04747124724-0.09729713549540.1592860231180.926697994471-0.04548770985640.938049229698-41.910780036-32.7023372085-10.3390700141
320.510316504337-1.990068256010.487609653864.7414981278-1.512407482021.1860679972-0.04719890199260.0475464798365-0.196177917757-0.04999449535020.001367288668910.3170776785430.289290798335-0.1267807242140.03798182873480.807900431698-0.2393681514410.03234217696610.809072544423-0.01337022544081.02359578295-30.3867489382-56.6431116553-15.8168708609
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 89 )AA9 - 891 - 81
22chain 'A' and (resid 90 through 122 )AA90 - 12282 - 114
33chain 'A' and (resid 123 through 163 )AA123 - 163115 - 155
44chain 'A' and (resid 164 through 184 )AA164 - 184156 - 176
55chain 'A' and (resid 185 through 201 )AA185 - 201177 - 193
66chain 'A' and (resid 202 through 228 )AA202 - 228194 - 220
77chain 'A' and (resid 229 through 247 )AA229 - 247221 - 239
88chain 'A' and (resid 248 through 275 )AA248 - 275240 - 267
99chain 'A' and (resid 276 through 308 )AA276 - 308268 - 300
1010chain 'A' and (resid 309 through 326 )AA309 - 326301 - 318
1111chain 'B' and (resid 8 through 104 )BB8 - 1041 - 97
1212chain 'B' and (resid 105 through 122 )BB105 - 12298 - 115
1313chain 'B' and (resid 123 through 146 )BB123 - 146116 - 139
1414chain 'B' and (resid 147 through 175 )BB147 - 175140 - 168
1515chain 'B' and (resid 176 through 228 )BB176 - 228169 - 221
1616chain 'B' and (resid 229 through 275 )BB229 - 275222 - 268
1717chain 'B' and (resid 276 through 305 )BB276 - 305269 - 298
1818chain 'B' and (resid 306 through 326 )BB306 - 326299 - 319
1919chain 'C' and (resid 8 through 146 )CC8 - 1461 - 139
2020chain 'C' and (resid 147 through 247 )CC147 - 247140 - 240
2121chain 'C' and (resid 248 through 325 )CC248 - 325241 - 318
2222chain 'a' and (resid 330 through 382 )aD330 - 3821 - 53
2323chain 'a' and (resid 383 through 392 )aD383 - 39254 - 63
2424chain 'a' and (resid 393 through 455 )aD393 - 45564 - 126
2525chain 'a' and (resid 456 through 501 )aD456 - 501127 - 172
2626chain 'b' and (resid 330 through 384 )bE330 - 3841 - 55
2727chain 'b' and (resid 385 through 404 )bE385 - 40456 - 75
2828chain 'b' and (resid 405 through 500 )bE405 - 50076 - 171
2929chain 'c' and (resid 330 through 351 )cF330 - 3511 - 22
3030chain 'c' and (resid 352 through 382 )cF352 - 38223 - 53
3131chain 'c' and (resid 383 through 392 )cF383 - 39254 - 63
3232chain 'c' and (resid 393 through 501 )cF393 - 50164 - 172

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る